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SMTL ID : 8tof.1

Rpd3S bound to an H3K36Cme3 modified nucleosome

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-2-2-2-2-2-mer

Ligands

1 x UNK- UNK- ARG- UNK- UNK: Rco1(Non-covalent)

UNK-UNK-ARG-UNK-UNK.1:

8 residues within 4Å:

Chain K: Y.58, E.62, D.91, E.93
Chain L: E.103, L.104, H.107, E.111

5 PLIP interactions:

4 interactions with chain K, 1 interactions with chain L

Hydrogen bonds: K:Y.58
Salt bridges: K:E.62, K:D.91, K:E.93
Hydrophobic interactions: L:E.103

1 x UNK- UNK- UNK- LYS- UNK- UNK- UNK: histone N-terminal tail(Non-covalent)

UNK-UNK-UNK-LYS-UNK-UNK-UNK.2:

15 residues within 4Å:

Chain A: V.787, G.794, F.795
Chain B: G.37, P.39, D.109, H.151, G.159, F.160, H.188, F.215, R.280, L.281, Y.313
Ligands: ZN.3

10 PLIP interactions:

9 interactions with chain B, 1 interactions with chain A

Hydrophobic interactions: B:D.109, B:F.160, B:F.160, B:F.215, B:F.215, B:L.281, A:V.787
Hydrogen bonds: B:D.109, B:D.109, B:H.151

5 x ZN: ZINC ION(Non-covalent)

ZN.3:	6 residues within 4Å: Chain B: D.186, H.188, D.274, G.311, Y.313 Ligands: UNK-UNK-UNK-LYS-UNK-UNK-UNK.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.186, B:D.186, B:H.188, B:D.274
ZN.4:	4 residues within 4Å: Chain F: C.263, C.266, H.283, C.286 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.263, F:C.266, F:H.283, F:C.286
ZN.5:	4 residues within 4Å: Chain F: C.417, C.420, H.448, C.451 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.417, F:C.420, F:H.448, F:C.451
ZN.6:	4 residues within 4Å: Chain F: C.440, C.443, C.466, H.469 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.440, F:C.443, F:C.466, F:H.469
ZN.7:	5 residues within 4Å: Chain F: C.275, T.277, C.278, C.303, C.306 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.275, F:C.278, F:C.303

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Markert, J.W. et al., Structure of the complete Saccharomyces cerevisiae Rpd3S-nucleosome complex. Nat Commun (2023)

Release Date

2024-01-17

Peptides

Transcriptional regulatory protein SIN3: A
Histone deacetylase RPD3: B
Chromatin modification-related protein EAF3: CD
Transcriptional regulatory protein RCO1: EF
Histone H3: IM
Histone H4: JN
Histone H2A: KO
Histone H2B 1.1: LP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
F

F
G

I
a

M
e

J
b

N
f

K
c

O
g

L
d

P
h

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Transcriptional regulatory protein SIN3

Histone deacetylase RPD3

Chromatin modification-related protein EAF3

Transcriptional regulatory protein RCO1

Histone H3

Toggle Identical (IM)

Histone H4

Histone H2A

Histone H2B 1.1

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
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Surface
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Outline
Fog

Background

Transparent

Resolution

Low
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